Rhodomicrobium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA685190 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Rhodomicrobium vannielii ATCC 17100 genome sequencing
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Project description:Lactobacillus casei is remarkably adaptive to diverse habitats. To understand the evolution and adaptation of Lb. casei strains isolated from different environments, the gene content of 22 Lb. casei strains isolated from various habitats (cheeses, n=8; plant materials, n=8; and human sources, n=6) were examined by comparative genome hybridization with an Lb. casei ATCC 334-based microarray. Comparative genome hybridization was performed against an Affymetrix custom microarray designed to include 2,661 (97%) chromosomal and 17 (85%) plasmid CDSs predicted to occur in Lb. casei ATCC 334, as well as all predicted CDSs in the draft Lb. helveticus CNRZ 32 genome. CDSs that were not included in the microarray design were all transposase-encoding genes.
2010-06-21 | E-GEOD-15030 | biostudies-arrayexpress
Project description:<p>Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes. We made predictions of the etiology of disease in individual subjects based on the properties and features of the recovered cellular genomes. Three subtypes of samples were observed. First were four patients with low diversity metagenomes that were predominated by one or more pathogenic E. coli strains. Annotation allowed prediction of pathogenic type in most cases. Second, five patients were co-infected with E. coli and other members of the Enterobacteriaceae, including antibiotic resistant Enterobacter, Klebsiella, and Citrobacter. Finally, several samples contained genomes that represented dark matter. In one of these samples we identified a TM7 genome that phylogenetically clustered with a strain isolated from wastewater and carries genes encoding potential virulence factors. We also observed a very high proportion of bacteriophage reads in some samples. The relative abundance of phage was significantly higher in healthy travelers when compared to TD patients. Our results highlight that assembly-based analysis revealed that diarrhea is often polymicrobial and includes members of the Enterobacteriaceae not normally associated with TD and have implicated a new member of the TM7 phylum as a potential player in diarrheal disease. </p>
| phs001352 | dbGaP
Project description:The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage, Sample GSM1551550). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.
2017-03-24 | GSE95797 | GEO
Project description:After the wild type strain of Vibrio natriegens ATCC 14048 (BioSample Nr. NCBI: SAMN03178087) was cured from prophages (as described in the material and methods section), the genomes of the resulted strains dvnp1, dvnp2 and vnp12 were sequenced. As a control, the genome of the wild type strain was also prepared and used for sequencing. The aim of the sequencing was to verify the deleted regions and to screen the genome for new mutations.
2019-07-01 | E-MTAB-7875 | biostudies-arrayexpress
Project description:Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Analysis of cotton variety planting statistics indicates a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv. malvacearum (Xcm) strains. Illumina based draft genomes were generated for thirteen Xcm isolates. These genomes, along with 4 previously published Xcm genomes, encode 24 conserved and nine variable type three effectors. Strains in the race 18 clade contain 3 to 5 more effectors than other Xcm strains. SMRT sequencing of two geographically and temporally diverse strains of Xcm yielded circular chromosomes and accompanying plasmids. These genomes encode eight and thirteen distinct transcription activator-like effector genes. RNA-sequencing revealed 52 genes induced within two cotton cultivars by both tested Xcm strains. This gene list includes a homeologous pair of genes, with homology to the known susceptibility gene, MLO. In contrast, the two strains of Xcm induce different class III SWEET sugar transporters. Subsequent genome wide analysis revealed patterns in the overall expression of homeologous gene pairs in cotton after inoculation by Xcm. These data reveal host-pathogen specificity at the genetic level and strategies for future development of resistant cultivars.
2017-07-24 | GSE101778 | GEO